# Total segmentator module returned with non-zero exit status 1 on to 5.12.1

**URL:** <https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634>\
**Category:** Support\
**Created:** [July 15, 2026, 12:22pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634 "2026-07-15T12:22:28Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![Cromwell](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@Cromwell](https://discourse.slicer.org/u/Cromwell)\
**Post date:** [July 15, 2026, 12:22pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/1 "2026-07-15T12:22:28Z")

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I’m having problems with the execution of the total segmentator module, I thought it was something installation, as version 5.10 was running I updated to 5.12.1 but it keeps the same error only with this module. I saw that some people have already reported problems with it! Trying to run lung nodules or lung segment airway and vessels I received the same error message

 ![IMG_9238](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/d/adcfa870ddd2e898d0ef0fc3f44c0a82ad77ab08.jpeg)

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**Author:** ![madsmess](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/madsmess/32/82617_2.png) [@madsmess](https://discourse.slicer.org/u/madsmess)\
**Post date:** [July 15, 2026, 4:28pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/2 "2026-07-15T16:28:24Z")

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My workaround for this problem was to uninstall Slicer, delete the app files from AppData, and reinstall Slicer inside the C drive (not in any subfolder, just inside the drive itself)

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<div class="post-metadata">

**Author:** ![Cromwell](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@Cromwell](https://discourse.slicer.org/u/Cromwell)\
**Post date:** [July 17, 2026, 9:04pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/3 "2026-07-17T21:04:05Z")

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I tried this, but nothing done! Already do the same error

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 18, 2026, 3:24pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/4 "2026-07-18T15:24:07Z")

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Please follow these instructions: [GitHub - lassoan/SlicerTotalSegmentator: Fully automatic total body segmentation in 3D Slicer using "TotalSegmentator" AI model · GitHub](https://github.com/lassoan/SlicerTotalSegmentator#failed-to-compute-results-error-the-first-time-trying-to-use-this-slicer-module)

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<div class="post-metadata">

**Author:** ![Cromwell](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@Cromwell](https://discourse.slicer.org/u/Cromwell)\
**Post date:** [July 18, 2026, 8:52pm UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/5 "2026-07-18T20:52:39Z")

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**I would like to share the solution that worked for me, as it may help other users and possibly identify a compatibility issue.**

I was using:

- **3D Slicer 5.12.2 (Windows)**
- **TotalSegmentator extension 2.13.0**
- **CPU inference (AMD GPU, no CUDA)**

The following tasks worked correctly:

- `total`

However, the following tasks consistently failed:

- `lung_nodules`
- `lung_vessels`

The errors were:

```auto

```

```auto
RuntimeError: Could not find requested nnUNetTrainer_MOSAIC_1k_QuarterLR_NoMirroring

```

and

```auto

```

```auto
RuntimeError: Could not find requested nnUNetTrainerSkeletonRecall

```

I tried all of the following without success:

- Force reinstall of the TotalSegmentator extension
- Re-downloading the model weights
- Deleting and downloading the datasets again
- Restarting Slicer multiple times

The downloaded models were correct, and the standard **total** task always worked.

Checking the installed package versions revealed:

```auto

```

```auto
TotalSegmentator: 2.13.0
nnunetv2: 2.8.1

```

The issue was resolved by downgrading **nnunetv2** to **2.6.2** from the Slicer Python Console:

```auto

```

```auto
slicer.util.pip_install("nnunetv2==2.6.2")

```

After restarting Slicer:

```auto

```

```auto
TotalSegmentator: 2.13.0
nnunetv2: 2.6.2

```

Everything worked correctly:

- ✅ total
- ✅ lung\_nodules
- ✅ lung\_vessels (vessels and airways)

This suggests that **TotalSegmentator 2.13.0 is currently not fully compatible with nnUNetv2 2.8.1 for tasks that rely on custom nnUNet trainers** , while it works correctly with **nnUNetv2 2.6.2**.

Hopefully this information helps other users experiencing the same issue and assists the developers in tracking the version compatibility problem.

Thank you for the excellent extension.

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<div class="post-metadata">

**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [July 19, 2026, 1:59am UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/6 "2026-07-19T01:59:45Z")

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Thanks for the information. It looks like the issue was resolved in TotalSegmentator 2.14.0.

> <https://github.com/wasserth/TotalSegmentator/commit/33a8cf2ff64a51eec9a1c148229985dd993d1d11>

SlicerTotalSegmentator will need to be updated to a newer version:

> <https://github.com/lassoan/SlicerTotalSegmentator/blob/bded9731643c684f2b930d9e480d458a5b0b680b/TotalSegmentator/TotalSegmentator.py#L429>

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 21, 2026, 1:07am UTC](https://discourse.slicer.org/t/total-segmentator-module-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/7 "2026-07-21T01:07:02Z")

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Thanks for the report and the investigation! I’ve pushed an update to the TotalSegmentator extension to update to 2.14.0.

> <https://github.com/lassoan/SlicerTotalSegmentator/commit/270cac20b78a282505e4f6a25d268666e4056019>
>
> Fixes the issue reported at
> https://discourse.slicer.org/t/total-segmentator-mod…ule-returned-with-non-zero-exit-status-1-on-to-5-12-1/47634/5
> 
> Package requirements (torch\>=2.1.2, nnunetv2\>=2.3.1) and the task/label
> maps in map\_to\_binary.py are unchanged from v2.13.0, so no other updates
> are needed.